POS0165 WHOLE EXOME SEQUENCING TO IDENTIFY RARE INFLAMMATORY VARIANTS IN AN IRISH COHORT WITH CHRONIC NONBACTERIAL OSTEOMYELITIS (CNO)
Authors: D. O’Leary, O. Killeen, A. G. Wilson
Journal: Annals of the Rheumatic Diseases (2022)

Background Chronic nonbacterial osteomyelitis (CNO) is a rare inflammatory disease affecting bone which predominantly occurs in the paediatric population. It is frequently associated with pustulosis, psoriasis, inflammatory bowel disease and arthritis, in particular enthesitis-related arthritis. Activation of the NLRP3 inflammasome has been implicated in both human and mouse models of the disease. Objectives To identify a candidate list of rare, deleterious variants in known inflammatory genes in an Irish cohort with CNO. Methods 41 unrelated Irish children with CNO were recruited. Whole exome sequencing was performed on blood using Agilent SureSelect XT Human All Exon V6 kits and Illumina HiSeq 3000 with 150bp paired-end reads. Reads were aligned to the hg19 reference genome. After preprocessing, variants were hard filtered using quality by depth(QD) &gt; 2.0, read depth (DP) &gt;10 and genotype quality (GQ) &gt;20. Synonymous variants and variants with MAF &gt; 0.01 were excluded from further analysis. Remaining variants were filtered against existing databases of genes known to be associated with inborn errors of immunity, autoimmunity or autoinflammation. The Gene Damage Index (GDI) was used to identify genes which are least tolerant to variance and CADD phred-like scores to identify variants predicted to be deleterious. Genes with variants in &gt;=2 CNO patients were included in the candidate list and variants manually checked using the Integrative Genomics Viewer (IGV). Results After filtering low-quality, synonymous and common variants, 17,293 variants were filtered against a database of 581 known inflammatory genes. 350 rare variants in 201 genes predicted to be intolerant to variance were identified. After excluding those present in one individual only, ranking by CADD phred-like scores and manual inspection on IGV, a candidate list of 25 genes remained. The same variant in IL17RA, NLRP1 and KMT2D was present in 3 unrelated individuals (Table 1). IL17RA belongs to the Th17 pathway which is involved in psoriasis pathogenesis. NLRP1 is implicated in several autoinflammatory diseases including psoriasis. None of the individuals carrying these variants in IL17RA or NLRP1 have psoriasis. One individual with IL17RA variant has 1 st -degree family history of psoriasis. Rare variants which are predicted to be deleterious were found in two individuals in each of the following genes in the IL-17 signalling/Th17 differentiation pathway: IL17RB, IL17RE, IL25, HIF1A (Table 1). This suggests that the Th17 pathway may play a role in disease pathogenesis in a proportion of children with CNO. Conclusion IL17 +/- the IL-17 signalling/Th17 differentiation pathways, and NLRP1 provide targets for further investigation in CNO. The role of these candidate genes may be further elucidated through gene-/pathway-based burden testing against a matched control population. References [1]McKenna A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep 1;20(9):1297–303. [2]Itan Y, et al. The human gene damage index as a gene-level approach to prioritizing exome variants. Proc Natl Acad Sci U S A. 2015;112(44):13615–20. [3]Rentzsch P, et al. CADD: Predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019 Jan 8;47(D1):D886–94. Table 1. Sample Gene Variant Effect CADD CNO MAF gnomAD MAF OR p-value 16 IL17RA 22- 17586757-T&gt;C Nonsynonymous 24.5 0.04 0.0034 11.06 0.003 37 p.W320R 42 5 NLRP1 17- 5462417- C&gt;A Nonsynonymous 26.2 0.04 0.0058 6.47 0.01 9 p.Q533H 38 2 KMT2D 12- 49434409-G&gt;A Nonsynonymous 21.3 0.04 0.0056 6.75 0.01 11 p.P2382S 21 10 IL17RB 3-53889368-G&gt;A Nonsynonymous 29.7 0.024 0.0061 4.05 0.09 40 p.G177R 7 IL17RE 3-9957033-C&gt;A Nonsynonymous 24.9 0.024 0.0086 3.19 0.13 43 pL400M 11 IL25 14-23845076-G&gt;A Nonsynonymous 34 0.024 0.0085 3.02 0.15 24 p.R174H 9 HIF1A 14-62187212-G&gt;C Nonsynonymous 23.7 0.024 0.0026 9.9 0.02 15 p.V74L Disclosure of Interests Daire O’Leary Grant/research support from: AbbVie SOBI Nordic Pharma Newman Fellowship in Rheumatology, Orla Killeen: None declared, Anthony G Wilson: None declared